Cavity-Type DNA Origami-Based Plasmonic Nanostructures for Raman Enhancement

Large-scale assembly of geometrically diverse metal nanoparticles-based 3D plasmonic DNA nanostructures for SERS detection of PNK in cancer cells

The organization of geometrically diverse metal nanoparticles into a core/satellite structure at a large scale is a promising strategy for improve SERS performance due to hot spots localized enrichment and signal increase. However, due to the lack of extensional frames and strong electrostatic repulsion between plasma NPs, the fabrication of such 3D architectures with a high-density periodic hotspot in the focus volume has proven exceedingly difficult. Herein, we demonstrate a facile large-scale assembly of geometrically diverse metal nanoparticles strategy for constructing spatially extended 3D plasmonic nanostructures resembling "signal towers" based on RCA-mediated periodic organization of gold nanospheres (GNS) surrounding gold nanorods (GNRs). Using cancer cell T4 PNK as a model, a padlock probe with 5'- hydroxyl (P-circle) was designed as the T4 PNK substrate. The center Au nanorod was coated with P1 and served as a "pedestal" to allow substantial loading of P-circle after target phosphorylation to initiate the rolling ring amplification reaction (RCA). The resultant DNA nanowire serves as an "antenna" to successively lock numerous Raman reporter P2 (Cy3-P2-SH) through base pairing at regular intervals. Finally, the 3D plasma DNA nanostructures that resemble "signal towers" could be obtained by placing a large number of GNS with a strong affinity for Au-S. The proposed 3D SERS sensor exhibited a sensitivity of LOD as low as 0.274 mU/mL, which was attributed to a substantial electromagnetic field enhancement at the inter-nanoparticle gaps between the adjacent pedestal and antenna. Moreover, by exploiting the synergistic effect of the periodically extended DNA scaffold generated by RCA amplification and the co-assembly of thiol ligand, the loaded GNS can be extended to three-dimensional space, forming a high-density periodic hotspot in the focal volume, thereby ensuring high enhancement and high reproducibility of Raman signals. In addition, this method can be used to quantify T4 PNK in HeLa cells, demonstrating its applicability in diagnosing and estimating PNK-related diseases in complex fluids.

DNA-mediated dynamic plasmonic nanostructures: assembly, actuation, optical properties, and biological applications

Recent advances in DNA technology have made it possible to combine with the plasmonics to fabricate reconfigurable dynamic nanodevices with extraordinary property and function. These DNA-mediated plasmonic nanostructures have been investigated for a variety of unique and beneficial physicochemical properties and their dynamic behavior has been controlled by endogenous or exogenous stimuli for a variety of interesting biological applications. In this perspective, the recent efforts to use the DNA nanostructures as molecular linkers for fabricating dynamic plasmonic nanostructures are reviewed. Next, the actuation media for triggering the dynamic behavior of plasmonic nanostructures and the dynamic response in optical features are summarized. Finally, the applications, remaining challenges and perspectives of the DNA-mediated dynamic plasmonic nanostructures are discussed.

Pattern Recognition Directed Assembly of Plasmonic Gap Nanostructures for Single-Molecule SERS

Gold nanocubes (AuNCs) with tunable localized surface plasmon resonance properties are good candidates for plasmonic gap nanostructures (PGNs) with hot spots (areas with intense electric field localization). Nevertheless, it remains challenging to create shape-controllable nanogaps between AuNCs. Herein, we report a DNA origami directed pattern recognition strategy to assemble AuNCs into PGNs. By tuning the position and number of capture strands on the DNA origami template, different geometrical configurations of PGNs with nanometer-precise and shape-controllable gaps are created. The localized field enhancement in these gaps can generate hot spots that are in accordance with finite difference time domain simulations. Benefiting from the single Raman probe molecule precisely anchored at these nanogaps, the dramatic enhanced electromagnetic fields localized in hot spots arouse stronger single-molecule SERS (SM-SERS) signals. This method can be utilized in the design of ultrahigh-sensitivity photonic devices with tailored optical properties and SERS-based applications.

A Label-Free Colorimetric Assay Based on Gold Nanoparticles for the Detection of H2O2 and Glucose

The significance of sensing hydrogen peroxide (H2O2) is due to its ubiquity, being a potential biomarker as well as an end-product of several oxidation reactions. Herein, based on gold nanoparticles (AuNPs) and coupled with single-stranded DNA (ssDNA) and ceria nanoparticles (CeO2), we developed a novel colorimetric method to detect H2O2 and glucose in NaCl solutions. In the presence of H2O2, ssDNA adsorbed on the surface of CeO2 could be released and subsequently decorated AuNPs, resulting in a distinct color change of the aqueous solution from purple to red, which could be observed by the naked eye. Since H2O2 can be produced in the process of glucose oxidation by glucose oxidase (GOx), this approach can also be employed to detect glucose. By employing this sensing system, the detection limits for H2O2 and glucose are about 0.21 μM and 3.01 µM, respectively. Additionally, monitoring the content of glucose in blood serum samples was successfully achieved by the proposed strategy. This work opens a potential avenue for the quantitative detection of H2O2 and glucose in clinical diagnostics.

SERS substrate fabrication for biochemical sensing: towards point-of-care diagnostics

Rapid technology development and economic growth have brought attention to public health issues, such as food safety and environmental pollution, which creates an ever-increasing demand for fast and portable sensing technologies. Portable surface-enhanced Raman spectroscopy (SERS) capable of various analyte detection with low concentration in a convenient manner shows advantages in sensing technology including enhanced diagnostic precision, improved diagnostic efficiency, reduced diagnostic cost, and alleviation of patient pain, which emerges as a promising candidate for point-of-care testing (POCT). SERS detection technology based on different nanostructures made of noble metal-based nanomaterials can increase the sensitivity of Raman scattering by 6-8 orders of magnitude, making Raman based trace detection possible, and greatly promote the application scenarios of portable Raman spectrometers. In this perspective, we provide an overview of fundamental knowledge about the SERS mechanism including chemical and electromagnetic field enhancement mechanisms, the design and fabrication of SERS substrates based on materials, progress of using SERS for POCT in biochemical sensing and its clinical applications. Furthermore, we present the prospective of developing new nanomaterials with different functionalities for advanced SERS substrates, as well as the future advancement of biomedical sensing and clinical potential of SERS technology.

Fabrication and SERS properties of complex and organized nanoparticle plasmonic clusters stable in solution

SERS activity can be increased by the formation of hot spots at the interparticle junctions of plasmonic nanoparticles in very close proximity, dramatically improving the enhancement factors in comparison with isolated nanoparticles. Controlling the number and geometrical architecture of hot spots, while endowing the clusters with colloidal stability, results in feasible optical sensors, able to provide quantitative SERS responses. Here, we review the approaches proposed to date to produce colloidal stable clusters, focusing on the control of the coordination number of nanoparticle assemblies and interparticle gaps. Clusters of spherical nanoparticles of the same size and rods of the same size are described to subsequently outline core-satellite constructs of nanoparticles of different sizes. Besides, purification processes for nanoparticle clusters are revised to provide efficient production in high yields.

Impact of the Interband Transitions in Gold and Silver on the Dynamics of Propagating and Localized Surface Plasmons

Understanding and modeling of a surface-plasmon phenomenon on lossy metals interfaces based on simplified models of dielectric function lead to problems when confronted with reality. For a realistic description of lossy metals, such as gold and silver, in the optical range of the electromagnetic spectrum and in the adjacent spectral ranges it is necessary to account not only for ohmic losses but also for the radiative losses resulting from the frequency-dependent interband transitions. We give a detailed analysis of Surface Plasmon Polaritons (SPPs) and Localized Surface Plasmons (LPSs) supported by such realistic metal/dielectric interfaces based on the dispersion relations both for flat and spherical gold and silver interfaces in the extended frequency and nanoparticle size ranges. The study reveals the region of anomalous dispersion for a silver flat interface in the near UV spectral range and high-quality factors for larger nanoparticles. We show that the frequency-dependent interband transition accounted in the dielectric function in a way allowing reproducing well the experimentally measured indexes of refraction does exert the pronounced impact not only on the properties of SPP and LSP for gold interfaces but also, with the weaker but not negligible impact, on the corresponding silver interfaces in the optical ranges and the adjacent spectral ranges.

DNA-Modulated Plasmon Resonance: Methods and Optical Applications

The near-field effects in the vicinity of metallic nanoparticle surfaces, as induced by electromagnetic radiation with specific wavelength, give rise to a variety of novel optical properties and attractive applications because of surface plasmons, which are the coherent oscillations of conduction electrons on a metal surface. The interdisciplinary field of plasmonics has witnessed vigorous growth, promoting research on the modulation of plasmon resonance by constructing advanced plasmonic nanoarchitectures with controllable size, morphology, or interparticle coupling. Among diversified tools, deoxyribonucleic nucleic acid (DNA) possesses prominent superiority as a result of its designability, programmability, addressability, and ease of nanomaterial modification. In this review, we focus on the methods and optical applications of plasmon resonance modulation accomplished by DNA nanotechnology. Recent developments in the construction of DNA-mediated plasmonic nanoarchitecture and key ongoing research directions utilizing unique optical features are highlighted. Obstacles and challenges in this field are pointed out, followed by preliminary suggestions on some areas of opportunity that deserve attention.

Plasmonic isomers via DNA-based self-assembly of gold nanoparticles

Developments in DNA nanotechnology offer control of the self-assembly of materials into discrete nanostructures. Within this paradigm, pre-assembled DNA origami with hundreds of DNA strands allows for precise and programmable spatial positioning of functionalised nanoparticles. We propose an alternative approach to construct multiple, structurally different, nanoparticle assemblies from just a few complementary nanoparticle-functionalised DNA strands. The approach exploits local minima in the potential energy landscape of hybridised nanoparticle-DNA structures by employing kinetic control of the assembly. Using a four-strand DNA template, we synthesise five different 3D gold nanoparticle (plasmonic) tetrameric isomers, akin to molecular structural isomers. The number of different structures formed using this approach for a set of DNA strands represents a combinatorial library, which we summarise in a hybridisation pathway tree and use to achieve deposition of tetrahedral assemblies onto substrates in high yield. The ability to program nanoparticle self-assembly pathways gives unprecedented access to unique plasmonic nanostructures.

Restriction Enzymes as a Target for DNA-Based Sensing and Structural Rearrangement

DNA nanostructures have been shown viable for the creation of complex logic-enabled sensing motifs. To date, most of these types of devices have been limited to the interaction with strictly DNA-type inputs. Restriction endonuclease represents a class of enzyme with endogenous specificity to DNA, and we hypothesize that these can be integrated with a DNA structure for use as inputs to trigger structural transformation and structural rearrangement. In this work, we reconfigured a three-arm DNA switch, which utilizes a cyclic Förster resonance energy transfer interaction between three dyes to produce complex output for the detection of three separate input regions to respond to restriction endonucleases, and investigated the efficacy of the enzyme targets. We demonstrate the ability to use three enzymes in one switch with no nonspecific interaction between cleavage sites. Further, we show that the enzymatic digestion can be harnessed to expose an active toehold into the DNA structure, allowing for single-pot addition of a small oligo in solution.